We have fenced areas where the ducks spend most of their time, with nice bedding that helps keep the natural breakdown of their poop moving along so there is very little odor. I have asked friends and neighbors to level with me and no one has said the aroma was anything but neutral to pleasant.
Water management in the shelter is a major step to keeping their housing from being nasty. I spend 15 minutes a day on room service for their night pen, then every week or two some extra time replacing bedding, either all (like today, and I am playing hooky right now) of it and that can take an hour or so, or in sections, spending an extra fifteen minutes and doing a section a day so it takes three days to do the whole thing.